Thomas's original ambition was to be a professional footballer. He achieved a place on the ground staff at Norwich City, playing as an inside forward. However an ankle injury forced him to give up playing. He was then persuaded to take up refereeing at the age of sixteen. He made rapid progress, reaching the Welsh League and in 1964 became a Football League linesman. Two years later aged only thirty he became a Football League referee, one of the youngest referees of the time .
Thomas officiated in both the 1974 and 1978 World Cups, and in the 1976 European Championship. During a long and sometimes controversial career as a referee in the old English First Division he was known as "The Book" for his strict interpretation of the laws of the game.
Thomas drew the ire of Ipswich fans when, during a 1975 FA Cup semi-final against West Ham, he disallowed a goal from Bryan Hamilton which seemed legitimate by giving offside despite a better-placed linesman not flagging for it. 
At the European Championship of 1976 in Yugoslavia, Thomas was the referee of the semi-final between Czechoslovakia and the Netherlands. In the extra time of that match, he failed to notice a rough foul by Antonín Panenka on Johan Cruyff, after which Zdenek Nehoda was able to score the decisive goal. The Dutch were furious about this decision, and Willem van Hanegem, who refused to play on, received a red card. In a 2008 documentary by the Dutch TV program Andere Tijden Sport, Thomas admitted he made a mistake by not noticing the foul.
Thomas drew the ire of Everton fans when, during a 1977 FA Cup semi-final against city rivals Liverpool, he disallowed a late goal, also from Bryan Hamilton, which seemed legitimate and had gone largely uncontested by even the Liverpool supporters, and would have taken Everton to the cup final as 3–2 winners.
He also blew the final whistle seconds before Zico of Brazil scored what would have been the winning goal from a corner in a 1978 World Cup match against Sweden. He was also strongly opposed to extravagant goal celebrations, going so far as to break up celebrations and order players back to their positions for the restart.
In the 1981 League Cup Final, Thomas allowed a goal from Liverpool defender Alan Kennedy 2 minutes from the end of extra time despite the fact that Sammy Lee, lying in an offside position, had to move his head to avoid being hit by the ball.
In 1984 he published his autobiography, By the Book.
- Clive Thomas (1984) By the Book, Collins Willow, p3
- Confirmation of place of residence during career: example from Welsh Football Data Archive website.
- Clive Thomas: "Mijn fout kostte Oranje EK-goud" (in Dutch)
- Disallowed goal for Everton v. Liverpool, 1977 FA Cup semi-final: Guardian Unlimited website.
- Disallowed goal for Brazil v. Sweden, World Cup 1978, : WorldCup365.com website.
- Autobiography, "By the Book": TMWMTT.com website.
- High Sheriff of Mid Glamorgan, 2004: BBC.co.uk website.